Initially one of the shared mailboxes was a user mailbox. That is how we discovered the problem. We have since changed that user mailbox type into the shared mailbox type to resolve the central storing of conversation history that was occurring.
These users are full access delegates to 4 different shared mailboxes. And the problem only appears to be effecting this workgroup.
Initially they wanted the one account to be a standard user mailbox so they could sync its calendar to their phones. Since we cannot sync the shared mailbox data via activesync.
Are there any registry keys for Skype for Business that control where conversation history is stored. Via the client there really isn't a granular option for selecting which folder to use. It just auto selects from the primary account I am assuming.